| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1933/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Sconify 1.29.1 (landing page) Tyler J Burns
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the Sconify package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Sconify.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Sconify |
| Version: 1.29.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Sconify_1.29.1.tar.gz |
| StartedAt: 2025-10-17 13:23:08 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 13:25:34 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 145.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Sconify.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Sconify_1.29.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.29.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Sconify’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
SconeValues 17.228 0.140 17.412
ImputeTesting 5.145 0.036 5.196
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
Sconify.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Sconify ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘Sconify’ ... ** this is package ‘Sconify’ version ‘1.29.1’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '/' Note: wrong number of arguments to 'asinh' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Sconify)
Sconify.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(Sconify)
>
> test_check("Sconify")
Read the 100 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.968000)!
Learning embedding...
Iteration 50: error is 50.297498 (50 iterations in 0.01 seconds)
Iteration 100: error is 48.858852 (50 iterations in 0.01 seconds)
Iteration 150: error is 49.780739 (50 iterations in 0.02 seconds)
Iteration 200: error is 50.198668 (50 iterations in 0.02 seconds)
Iteration 250: error is 48.066923 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.009568 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.378140 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.185495 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.176490 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.173123 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.167723 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.166857 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.162968 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.163704 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.165242 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.158152 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.154467 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.153749 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.153652 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.152811 (50 iterations in 0.01 seconds)
Fitting performed in 0.26 seconds.
Read the 1000 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.15 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.376473 (50 iterations in 0.39 seconds)
Iteration 100: error is 60.680069 (50 iterations in 0.31 seconds)
Iteration 150: error is 60.334170 (50 iterations in 0.33 seconds)
Iteration 200: error is 60.213576 (50 iterations in 0.33 seconds)
Iteration 250: error is 60.154188 (50 iterations in 0.33 seconds)
Iteration 300: error is 1.342910 (50 iterations in 0.28 seconds)
Iteration 350: error is 1.226670 (50 iterations in 0.24 seconds)
Iteration 400: error is 1.194875 (50 iterations in 0.24 seconds)
Iteration 450: error is 1.184352 (50 iterations in 0.23 seconds)
Iteration 500: error is 1.177972 (50 iterations in 0.24 seconds)
Iteration 550: error is 1.173632 (50 iterations in 0.23 seconds)
Iteration 600: error is 1.170170 (50 iterations in 0.24 seconds)
Iteration 650: error is 1.167460 (50 iterations in 0.23 seconds)
Iteration 700: error is 1.164553 (50 iterations in 0.22 seconds)
Iteration 750: error is 1.162285 (50 iterations in 0.22 seconds)
Iteration 800: error is 1.160079 (50 iterations in 0.23 seconds)
Iteration 850: error is 1.158444 (50 iterations in 0.22 seconds)
Iteration 900: error is 1.157301 (50 iterations in 0.23 seconds)
Iteration 950: error is 1.155853 (50 iterations in 0.23 seconds)
Iteration 1000: error is 1.154722 (50 iterations in 0.22 seconds)
Fitting performed in 5.17 seconds.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 72 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 72 ]
>
> proc.time()
user system elapsed
30.143 0.466 31.092
Sconify.Rcheck/Sconify-Ex.timings
| name | user | system | elapsed | |
| FcsToTibble | 0.181 | 0.000 | 0.184 | |
| Fnn | 0.259 | 0.180 | 0.440 | |
| GetKnnDe | 0.104 | 0.000 | 0.104 | |
| GetMarkerNames | 0.034 | 0.004 | 0.039 | |
| ImputeTesting | 5.145 | 0.036 | 5.196 | |
| MakeHist | 0.682 | 0.036 | 0.720 | |
| MakeKnnList | 0.451 | 0.044 | 0.496 | |
| MeaningOfLife | 0 | 0 | 0 | |
| ParseMarkers | 0.300 | 0.019 | 0.326 | |
| PostProcessing | 0.112 | 0.008 | 0.120 | |
| ProcessMultipleFiles | 0.146 | 0.008 | 0.157 | |
| QuantNormalizeElements | 0.248 | 0.012 | 0.262 | |
| SconeValues | 17.228 | 0.140 | 17.412 | |
| SplitFile | 0.092 | 0.008 | 0.100 | |
| StringToNumbers | 0 | 0 | 0 | |
| SubsampleAndTsne | 2.893 | 0.008 | 2.909 | |
| TsneVis | 0.257 | 0.016 | 0.273 | |